Capillary electrophoresis is essential for Microsatellite marker based detection and quantification of adulteration of basmati rice (Oryza sativa)

Microsatellite markers are employed for genotyping of Basmati varieties and assaying purity of market samples. However, employment of diverse electrophoresis techniques across laboratories has resulted in inconsistent allele sizes, creating doubts about the suitability of the assay. This study evaluated agarose gel electrophoresis, slab gel electrophoresis, and capillary electrophoresis techniques for their efficiency in the detection and quantification of adulteration in Basmati samples. Comparative analysis across 8 microsatellite loci in 12 rice varieties demonstrated that the capillary electrophoresis method showed less error (+/- 0.73 bp) in the estimation of allele sizes compared to slab gel (+/- 1.59 bp) and agarose gel (+/- 8.03 bp) electrophoretic methods. Capillary electrophoresis showed greater reproducibility (< 0.5 bp deviation) compared to slab gel (1 bp) and agarose (> 3 bp) based methods. Capillary electrophoresis was significantly superior in quantification of the adulterant, with a mean error of +/- 3.91% in comparison to slab gel (+/- 6.09%). Lack of accuracy and consistency of the slab gel and agarose electrophoretic methods warrants the employment of capillary electrophoresis for Basmati rice purity assays.